I run the environmental genetics program in the Levi Lab at Oregon State University. We use separate facilities for pre-PCR and post-PCR genetics work and multiple UV-irradiated laminar-flow PCR cabinets to reduce the risk that environmental samples are contaminated. In our lab we primarily work with fecal DNA, environmental DNA (eDNA) from water filters, and DNA in residual saliva.
Ongoing eDNA projects are focused on testing and calibrating DNA in water as a tool to quantify fish abundance and phenology. These include two projects in Southeast Alaska where for three years we have compared weir counts of salmon passage with the DNA concentrations of each salmon species, and three years of eulachon population monitoring with mark-recapture paired with synchronous eDNA samples. We are also using eDNA to monitor eulachon run timing and relative abundance on the Columbia River.
We have several projects that use DNA from residual saliva. We have recently used eDNA from residual saliva on Devil’s Club berry stalks to determine the degree to which brown bears and black bears consume this fruit, and eDNA from saliva on partially consumed salmon carcasses as a source of high-quality DNA for genotyping bears in order to estimate population density and identify the bears that use salmon streams.
Recent work with fecal DNA includes genotyping of brown bears for population density estimation in the Chilkoot River Valley, Southeast Alaska, and an array of diet analyses using DNA metabarcoding
We are using DNA metabarcoding, a method that amplifies barcode genes from bulk DNA samples to identify the species within the sample using high-performance computing, to conduct diet analyses for bats, coastal martens, and Alexander Archipelago wolves.
Wheat, R.E., Allen, J.M., Miller, S.D.L, Wilmers, C.C., Levi, T. In review. Environmental DNA from residual saliva for efficient noninvasive genetic monitoring of brown bears (Ursus arctos). Molecular Ecology Resources
Levi, T., Wheat, R., Allen, J.M., Wilmers, C.C. 2015. Differential use of salmon by vertebrate consumers: implications for conservation. PeerJ. 3:E1157
Kuo, D.S., Labelle-Dumais, C., Mao, M., Jeanne, M., Kauffman, W.B., Allen, J., Favor, J. and Gould, D.B., 2014. Allelic heterogeneity contributes to variability in ocular dysgenesis, myopathy and brain malformations caused by Col4a1 and Col4a2 mutations. Human molecular genetics, 23(7), pp.1709-1722.
Million-Weaver, S., Alexander, D.L., Allen, J.M. and Camps, M., 2012. Quantifying plasmid copy number to investigate plasmid dosage effects associated with directed protein evolution. Microbial Metabolic Engineering: Methods and Protocols, pp.33-48.
Guthrie, V.B., Allen, J., Camps, M. and Karchin, R., 2011. Network models of TEM β-lactamase mutations coevolving under antibiotic selection show modular structure and anticipate evolutionary trajectories. PLoS Comput Biol,7(9), p.e1002184.
Allen, J.M., Simcha, D.M., Ericson, N.G., Alexander, D.L., Marquette, J.T., Van Biber, B.P., Troll, C.J., Karchin, R., Bielas, J.H., Loeb, L.A. and Camps, M., 2011. Roles of DNA polymerase I in leading and lagging-strand replication defined by a high-resolution mutation footprint of ColE1 plasmid replication. Nucleic acids research, 39(16), pp.7020-7033.
Troll, C., Alexander, D., Allen, J., Marquette, J. and Camps, M., 2011. Mutagenesis and functional selection protocols for directed evolution of proteins in E. coli. JoVE (Journal of Visualized Experiments), (49), pp.e2505-e2505.